Hello,
Sorry to revive a old topic but I have the same issue, and so I thought I'd add my details in case anyone has more info since last time:
Raspberry PI 3B
Retropie 4.3
BLE Keyboard Logitech K830
As OP, the keyboard is discovered and it claim pairing is successful, but it's not usable :(.
I found the post below on stack Exchange that looks promising (suggesting installing latest BlueZ module), but before I attempt the steps myself, I wanted to check if anyone has tried it for retropie.
"Does RPi 3 have BLE (Bluetooth Low Energy/Bluetooth 4.0/Bluetooth Smart)"
https://raspberrypi.stackexchange.com/questions/61758/does-rpi-3-have-ble-bluetooth-low-energy-bluetooth-4-0-bluetooth-smart#answer-61775
Thanks!
Tim